"I ask Mr. [Mahmoud] Ahmadinejad [the Iranian president] not to allow politicians to have sports positions so that this failure ends," Mehr news agency quoted Qalenoei as saying on Tuesday.
"I want to ask why successful managers are dismissed very easily to give their place to politicians who have caused all the failures," he added.
"I know I might lose my job by saying these things but the problems must be brought up so that somebody could do something about the current situation."
The former Esteqlal coach also pointed out that he left the Blues for having problems with such politicians who had dominated the club.
"I have no problem with Esteqlal. My problem is with those who have gained their current positions in the club with the support of such politicians," he said.
Qalenoei, nicknamed the General, has recently signed an agreement with Sepahan FC, after he clinched the Iranian Premier League (IPL) title with as Esteqlal manager.
He reportedly left Esteqlal due to disagreements with the club's chief executive Amir-Reza Veaz Ashtiani.